4,162 research outputs found
Hinge-bending motion of D-allose-binding protein from Escherichia coli - Three open conformations
No full textConformational changes of periplasmic binding proteins are essential for their function in chemotaxis and transport. The allose-binding protein from Escherichia coli is, like other receptors in its family, composed of two alpha/beta domains joined by a three-stranded hinge. In the previously determined structure of the closed, ligand-bound form (Chaudhuri, B. N., Ko, J., Park, C., Jones, T. A., and Mowbray, S. L. (1999) J. Mol. Biol. 286, 1519-1531), the ligand-binding site is buried between the two domains. We report here the structures of three distinct open, ligand-free forms of this receptor, one solved at 3.1-Angstrom resolution and two others at 1.7-Angstrom resolution. Together, these allow a description of the conformational changes associated with ligand binding. A few large, coupled torsional changes in the hinge strands are sufficient to generate the overall bending motion, with only minor disruption of the individual domains. Integral water molecules appear to act as structural "ball bearings" in this process. The conformational changes of the related ribose-binding protein follow a distinct pattern. The observed differences between the two proteins can be interpreted in the context of changes in sequence and in crystal packing and provide new insights into the nature of hinge bending motion in this class of periplasmic binding proteins
Structure of D-allose binding protein from Escherichia coli bound to D-allose at 1.8 angstrom resolution
No full textABC transport systems for import or export of nutrients and other substances across the cell membrane are widely distributed in nature. In most bacterial systems, a periplasmic component is the primary determinant of specificity of the transport complex as a whole. We report here the crystal structure of the periplasmic binding protein for the allose system (ALBP) from Escherichia coli, solved at 1.8 Angstrom resolution using the molecular replacement method. As in the other members of the family (especially the ribose binding protein, REP, with which it shares 35% sequence homology), this structure consists of two similar domains joined by a three-stranded hinge region. The protein is believed to exist in a dynamic equilibrium of closed and open conformations in solution which is an important part of its function. In the closed ligand-bound form observed here, D-allose is buried at the domain interface. Only the beta-anomer of allopyranose is seen in the crystal structure, although the alpha-anomer can potentially bind with a similar affinity. Details of the ligand-binding cleft reveal the features that determine substrate specificity. Extensive hydrogen bonding as well as hydrophobic interactions are found to be important. Altogether ten residues from both the domains form 14 hydrogen bonds with the sugar. Ln addition, three aromatic rings, one from each domain with faces parallel to the plane of the sugar ring and a third perpendicular, make up a hydrophobic stacking surface for the ring hydrogen atoms. Our results indicate that the aromatic rings forming the sugar binding cleft can sterically block the binding of any hexose epimer except D-allose, 6-deoxy-allose or 3-deoxy-glucose; the latter two are expected to bind with reduced affinity, due to the loss of some hydrogen bonds. The pyranose form of the pentose, D-ribose, can also fit into the ALBP binding cleft, although with lower binding affinity. Thus, ALBP can function as a low affinity transporter for D-ribose. The significance of these results is discussed in the context of the function of allose and ribose transport systems. (C) 1999 Academic Press
Apogon aurolineatus Mowbray
No full textApogon aurolineatus (Mowbray) Identification. Four adult specimens of A. aurolineatus provided the basis for genetic identification of seven larvae and one juvenile (Appendix 1, one adult is shown in Fig. 24). Adult A. aurolineatus can be distinguished from other Apogon by the combination of eight segmented anal-fin rays, 10–11 gill rakers on the lower limb of the first gill arch, 16–18 circum-caudal-peduncle scales, no dark markings or saddles on the posterior portion of the body, and two to four short dark lines radiating from the eye (Böhlke & Chaplin 1993; Gon 2002). Juveniles (Fig. 25). The single juvenile, a reared specimen of 12 mm SL, has a pale salmon body color, and the opercular and abdominal regions are silvery. In preservative, there are no distinctive markings except a few melanophores on top of the head. There are 11 gill rakers on the lower limb of the first gill arch. Comparisons Among Juveniles. Of the Apogon species for which juveniles are known, A. aurolineatus most closely resembles A. quadrisquamatus in lacking dark blotches or markings on the body. The reared juvenile of A. aurolineatus can be separated from juvenile A. quadrisquamatus in having a pale body color (vs. orange in A. quadrisquamatus), in lacking yellow on the dorsal and caudal fins, and in lacking an orange spot on the center of the caudal peduncle. Preserved juveniles of the two species are very similar, but eye diameter may be useful in separating the species (diameter of bony orbit approximately 13 % SL in the 12.0-mm SL juvenile of A. aurolineatus vs. 15 % SL in 14.0–16.0-mm SL juveniles of A. quadrisquamatus). Preserved juveniles of A. aurolineatus also are similar to those of A. robbyi and A. mosavi in having a pale body, but A. aurolineatus lacks the blotch of melanophores on the caudal peduncle present in those species. Larvae (Fig. 26). Apogon aurolineatus larvae genetically analyzed in this study are all approximately 8 mm SL. They are bright orange in life and have orange pelvic, anal, and second dorsal fins. The first dorsal fin is orange at the base, but most of the fin is bright yellow. The pectoral and caudal fins are clear. There are some pale areas on the head—below the anterior portion of the eye and above the tip of the snout. The top of the head has yellow pigment in some specimens. There are no dark markings on the body except sometimes a few melanophores on the top of the head. There are barely observable melanophores scattered on the jaws. The caudal-peduncle length ranges from 27 to 29 % SL. Comparisons Among Larvae. Fresh specimens of A. aurolineatus larvae are easily distinguished from other known Apogon larvae by the combination of bright orange body coloration and yellow pigment on the first dorsal fin. Preserved specimens usually have fewer melanophores on top of the head than larvae of other Apogon (zero to several vs. many) and a shorter caudal peduncle (27–29 % SL vs. 30–40 % SL in other species). Apogon robinsi Böhlke and Randall Identification. One adult specimen of A. robinsi was collected and analyzed genetically (Appendix 1). Because the photograph of that specimen is not of good quality, we selected a photograph of a specimen not included in the genetic analysis to represent the species (Fig. 27). Adult A. robinsi can be distinguished from other Apogo n species by the combination of eight segmented anal-fin rays, body and lateral-line scales of similar size, body with two distinct dark markings (one bar below and just behind second-dorsal fin and a bar on the posterior part of caudal peduncle—the distance between the two bars larger than the width of the posterior bar), and premaxillary dentition extending outside the mouth laterally on the bone (Böhlke & Chaplin 1993, Gon 2002). No larvae or juveniles analyzed in this study genetically match A. robinsi.Published as part of Baldwin, Carole C., Brito, Balam J., Smith, David G., Weigt, Lee A. & Escobar-Briones, Elva, 2011, Identification of early life-history stages of Caribbean Apogon (Perciformes: Apogonidae) through DNA Barcoding, pp. 1-36 in Zootaxa 3133 on pages 21-23, DOI: 10.5281/zenodo.27942
CR1 Knops blood group alleles are not associated with severe malaria in the Gambia
No full textThe Knops blood group antigen erythrocyte polymorphisms have been associated with reduced falciparum malaria-based in vitro rosette formation (putative malaria virulence factor). Having previously identified single-nucleotide polymorphisms (SNPs) in the human complement receptor 1 (CR1/CD35) gene underlying the Knops antithetical antigens Sl1/Sl2 and McC(a)/McC(b), we have now performed genotype comparisons to test associations between these two molecular variants and severe malaria in West African children living in the Gambia. While SNPs associated with Sl:2 and McC(b+) were equally distributed among malaria-infected children with severe malaria and control children not infected with malaria parasites, high allele frequencies for Sl 2 (0.800, 1,365/1,706) and McC(b) (0.385, 658/1706) were observed. Further, when compared to the Sl 1/McC(a) allele observed in all populations, the African Sl 2/McC(b) allele appears to have evolved as a result of positive selection (modified Nei-Gojobori test Ka-Ks/s.e.=1.77, P-valu
Quantum and its irreducible representations
No full textWe define for real a unital -algebra
quantizing the universal enveloping
-algebra of . The -algebra
is realized as a -subalgebra of the
Drinfeld double of and its dual Hopf -algebra
, generated by the equatorial Podle\'s sphere coideal
-subalgebra of and
its associated orthogonal coideal -subalgebra . We then classify all the irreducible
-representations of .Comment: 22 pages; author accepted manuscrip
On the sheaf-theoretic SL(2, C) Casson–Lin invariant
No full textWe prove that the (τ-weighted, sheaf-theoretic) SL(2, C) Casson–Lin invariant introduced by Manolescu and the first author is generically independent of the parameter τ and additive under connected sums of knots in integral homology 3-spheres. This addresses two questions asked by Manolescu and the first author. Our arguments involve a mix of topology and algebraic geometry, and rely crucially on the fact that the SL(2, C) Casson–Lin invariant admits an alternative interpretation via the theory of Behrend functions.</p
Candidatus Rhetoricae (or Novus Candidatus).
No full textThis little book is a find whatever it finally turns out to be! For now it seems to be a Jesuit collegium text in rhetoric following the Progymnasmata of Aphthonius. If one works from the back of the book, there is an apparently independent 48-page work, Angelus Pacis by Nicolas Caussini (Latinized name), S.J. The rest of the book seems to be a commentary on or presentation of Aphthonius' Progymnasmata in 3 parts covering 435 pages, followed by a T of C and an AI, which is often one page off. Pars II is titled Rhetoricae Praecepta, Pars III De Panegyrico seu Laudatione. Pars I seems to be Apparatus ad Fabulam et Narrationem. Fable is handled on 15-31. After the famous Greek definition of Theion done into Latin ( sermo falsus veritatem effingens ), the author distinguishes rational (human) and moral (animal) fables, with mixed fables including both. He holds (19) that the sense of the fable generally needs to be expressed; otherwise people often miss the point of a fable. His Latin for promythium is praefabulatio, for epimythium affabulatio. Apologus and parabola are identical for him with fabula. After describing the qualities and uses of fables, the author presents some nine fables that exemplify various levels of style, twice telling the same stories on two levels (WL and FC). The last example is of the florid style: The Silkworm and the Spider takes four pages to tell! I found this book sitting in a box of disparate, unmarked, old books. It pays to look!This is a hardbound book (hard cover)Language note: Bilingual: Greek/LatinElzevers
Searches for New Physics effects in b →sl-sl+ transitions
No full textThe dissertation aims at presenting the current situation in the measurements of electroweak
penguin diagrams dominated decays: b → sl−l+1 . These decays have been a smoking gun
for hunting for New Physics effects over many years, but in the last three years the research
on these phenomena has intensified due to new measurements. Enormous progress has
been made both on the theoretical and the experimental sides to understand the measured
deviations from the current Standard Model predictions, referred to in what follows as
“anomalies”. The author of this dissertation has been one of the main authors of the angular analysis
of B0→ K∗ 0µ+µ− decay in the LHCb experiment, which has been widely regarded as one
of the most important results of the flavour physics sector in recent years. He has proposed
a method called “the method of moments” to measure the angular terms of this decay,
which he has later successfully applied in the measurement itself. Moreover, he has been
the driving force behind the two other important analyses in LHCb: the measurement of
the angular distribution and branching ratio of the B0→ K∗ 0 (1430)µ+µ− decay, where again the method of moments has been used to obtain the angular coefficients, and the search for the light scalar particle that can be produced in the b → s transitions and that decays to a dimuon pair. In this case no signal has been observed and the upper limits on the branching fraction have been set, later to be used for constraining the inflaton model.
The dissertation is organized as follows: the brief introduction is followed by, the second
chapter devoted to a theoretical description of rare B decays, where the effective field
theory formalism is introduced. Furthermore, the author discusses the current theoretical
problems in calculating the Standard Model predictions for the b → sl−l+ processes. Last but not least, the optimised angular observables that are less dependent on the form
factors uncertainness are derived. The third chapter describes the experimental apparatus
used in the b → sl−l+ measurements. Special focus is put on the sub-detectors that play
an important role in the studies of b → sl−l+ transitions. Chapters 4, 5, 6 are devoted to
describing the data analyses performed by the author in the LHCb experiment. In Chapter 7
the global analysis of electroweak penguin decays is presented. This kind of global analysis
has become extremely popular in the past few years as it helps to constrain and pin down those New Physics models that are likely to be responsible for the observed anomalies. The
author of this monograph is involved in one of the biggest collaborations performing New
Physics fits, where he is the convenor of the Flavour Working group. Furthermore, the
author presents his own study on separating the long distance effects in the B0→ K∗ 0µ+µ−decay. This is the state of the art way of determining those contributions. The chapter ends with a description of possible New Physics models that can explain the observed discrepancies
contravariant function-valued valuations on polytopes
No full textWe present a complete classification of contravariant,
-valued valuations on polytopes, without any
additional assumptions.It extends the previous results of the second author
[Int. Math. Res. Not. 2020] which have a good connection with the and
Orlicz Brunn-Minkowski theory. Additionally, our results deduce a complete
classification of contravariant symmetric-tensor-valued
valuations on polytopes
The Laurent Extension of Quantum Plane: a Complete List of Uq(sl₂)-Symmetries
No full textThis work finishes a classification of Uq(sl₂)-symmetries on the Laurent extension Cq[x±¹,y±¹] of the quantum plane. After reproducing the partial results of a previous paper of the author related to symmetries with non-trivial action of the Cartan generator(s) of Uq(sl₂) and the generic symmetries, a complete collection of non-generic symmetries is presented. Together, these collections constitute a complete list of Uq(sl₂)-symmetries on Cq[x±¹,y±¹].The author would like to thank the anonymous referees for a large number of comments and suggestions that substantially improved the initial version of this paper
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